MetageneCluster

MetageneCluster generates metagene analysis plots for a given feature within a .gff/.gtf file when paired with a corresponding SAM file.

Table of Contents

1. About The Project
   • Built With
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. License
5. Contact

About The Project

Built With

• Python3
• MatPlotLib
• Numpy

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Getting Started

Python3 is required to install and run this program.

Prerequisites

Run in a terminal:

pip3 install matplotlib numpy

Installation

Clone the repo:

git clone https://github.com/aasaporito/MetageneCluster.git

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Usage

To run, open a terminal in the MetageneCluster directory.

Examples:

Minimal parameters:

  python3 run.py RNA_seq.sam hg38.gff CDS 500 1000

Full parameters:

  python3 run.py -c -s -r H3K36me3.sam input.sam TAIR9.gff CDS 500 1000 0.25

Parameters

Argument	Function
-c, -u, -cu	Indicates whether you want to cluster your data by similarity. May be set to -c to produce clustered metagene plots, -u to produce a single, unclustered metagene plot or -cu to produce both an unclustered as well as clustered plots. Default: -c.
-s, -m	Indicates whether you want to cluster by shape only or include magnitude. May be set to -s to cluster by overall shape of plot or -m to factor magnitude of signal into account when clustering. Meaningless in unclustered mode. Default: -s.
-r, -R	Indicates that you want to compute and plot the ratio of the first alignment file to the second. If -r or -R are enabled, you must follow with two .sam files. Default: disabled.
file_name.sam	Your input aligned .sam file with path. Must be two files separated by whitespace if -r is enabled.
file_name.gff	Your input annotation file file with path.
feature	The feature you want to build your metagene plots from. i.e. gene, CDS.
streamDistance	Integer distance up and downstream of your feature of interest to be included in the plot. Included for context only, not used for caluclating which features cluster together.
norm_length	Integer length in nucleotides that features should be normalized to.
dist_reduct	Used to determine how many clusters, k, to build. The method selects the cluster number when the change in total distance from the last cluser number, k-1, has a smaller reduction than this value. Must be between 0 and 1. Default: 0.25

The program will store all generated output in ~/MetageneCluster/Outputs/

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License

Distributed under the Mozilla Public License Version 2.0 License. See LICENSE.txt for more information.

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Contact

Primary Author:

Clayton Carter - LinkedIn - GitHub

Current Maintainer:

Aaron Saporito - LinkedIn - GitHub

Project Link: https://github.com/aasaporito/MetageneCluster

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